What we’ve learned about genomics . . . so far

What we’ve learned about genomics . . . so far

Three years ago, genomic testing became available and changed the genetics industry. Four experts recently shared their experiences in a town hall meeting.

by Danielle BrownBrown is a senior at the University of Wisconsin-Madison majoring in dairy science and life sciences communications. She is the 2011 Hoard’s Dairyman editorial intern.

Genomic technology has the potential to control inbreeding, discover haplotypes, and find genes that affect heat stress.

A lot has changed since genomics hit the press in April 2008 and evaluations became official the following January. Despite genomics rapid utilization, many questions remain. As with any technology, new discoveries and the tweaking of current methods change the applications.

A four-person panel, including USDA-Agricultural Research Service (ARS) research geneticist Curt Van Tassell, Charlie Will from Select Sires, Jay Jauquet with Alta Genetics, and Tom Schmitt of Morningview Holsteins, shared their insight about the technology at a town hall meeting organized by the Wisconsin Holstein Association this July.

Three years later
Currently, about 5,000 animals are being genomic tested each month, according to Van Tassell, and this number continues to grow. Tested animals are predominantly registered Holsteins, Jerseys, and Brown Swiss. They are tested at a young age. A greater number of Holsteins have been tested, but a larger percentage of the Jersey breed has genomic test results.

Initially, the only test available was the 50K (meaning 50,000 markers) test which was not very cost-effective. But, it boosted reliability from traditional parent averages. There are now other options available on the market. The most popular is the 3K chip; a cheaper, lower-density, and less-accurate model. Generally available for less than $50. It serves a variety of purposes, including parent verification, inbreeding avoidance, and the possibility of making better mating decisions.

There are also higher-density chips (more than 700,000 markers) available. Despite its considerable cost, these chips provide a considerable leap in reliability.

The A.I. industry was one of the earliest adopters of the technology and now uses it extensively when acquiring young bulls. In fact, some bulls are marketed based entirely on genomic data.

Current applications
In the A.I. industry, genomics has improved the precision for predicting progeny test graduates. Select Sires’ Charlie Will shared a study in which he ranked bulls solely on genomic results, and then waited for the bulls to have daughter information. He noticed that the genomic results were an accurate predictor of future rank among the graduating class. Although there were a few changes in the final ranking, bulls predicted to be in the lowest quartile of their class never finished in the top quartile and vice versa.

“In the past three years, we have learned that the numbers may change slightly when young bulls get progeny proofs, but the rank to one another rarely changes,” he said.

Jauquet shared his experiences buying bulls for Alta Genetics, as well as breeding and developing cattle at his family’s 300-cow farm, Synergy Dairy at Pulaski, Wis. He urged producers to look beyond an animal’s GTPI (genomic total performance index) or $NM (Net Merit) values. He encouraged breeders to use the whole genomic profile to find the best mating.

“Producers can use genomics to do so much more than fill A.I. contracts,” he explained. “Find the traits you want in your herd. Don’t be afraid to use a lower GTPI young sire if you are breeding for a different trait.”

At his family’s farm, they focus on finding the best heifers to flush and produce future offspring. All top calves (based on parent average) are tested with the 3K test. Once those results are returned, the animal(s) that surpassed expectations are tested with the 50K chip. Based on the results of the higher reliability test, females are then flushed.

Schmitt, whose 90-cow dairy is located in Durango, Iowa, was initially slow to adopt the technology in his herd. He doubted the technology could be of any use to him or expand his herd’s marketing potential. Only when he saw a drop in the number of embryo sales, and the necessity of using it to secure A.I. contracts, did he implement the technology.

“Today, I use the genomic test to sort out which heifers I will work with in my flush program,” Schmitt explained. “It has been very accurate.”

Genetic treadmill
“The treadmill of genetic improvement will keep accelerating, and top animals in the breed will stay there for a much shorter amount of time,” Van Tassell told the crowd.

Using the popular Holstein sire O-Man as an example, he commented that it would be very unlikely a bull would remain at the top of the list for multiple proofs.

“Genomics adds significant value to some animals and finds some animals and families that were not previously identified,” Will said.

Imported genetics also may play a role in unintentional acceleration or overinflation of predicted transmitting abilities which was a concern raised by those attending the forum.
“We can’t predict genotypes we’ve never seen before,” explained Van Tassell. “We must be cautious of genomic predictions on the outer fringes, such as unusually high- or low-ranking animals.”

Future developments
Genomic technology has the potential to be used for a wide variety of purposes. It can be a tool used to control inbreeding depression. It can also continue to discover haplotypes (small chunks of a single-strand DNA) that can have an unfavorable effect on some traits but possibly enhance others. (See the August 25, 2011, issue, page 528.)

Van Tassell and his lab are developing a larger variety of genomic tests. His goal is to develop a low-cost test (less than $5) so more animals can be tested cost-effectively. Genomic testing in these situations can help farmers verify parent identification and lead to better matings. Additionally, farmers could sort heifers into groups and determine what animals to use the best semen on and which ones to possibly cull or use as recipients for embryos.

One step in that direction will be a low-density, 6,000-marker chip available later this fall. It will offer more reliability than the 3K chip but still be a low-cost option.

No matter how far this technology goes, there will still be a need for performance information, says Van Tassell.

“Genomics is a dynamic, random-based process that only becomes accurate with more daughters,” explained Van Tassell. “It is absolutely critical to use performance data, the gold standard, to calibrate the system.”

The other panelists agreed that genomics is not the only factor in marketing quality genetics or making breeding decisions.

“Genomics is a tool. You still have to have a great cow family and individual to bring the most money,” commented Schmitt. “Everyone has something at home that with the right mating can produce those high-ranking heifers.”

“Don’t forget what you’ve learned in the last 30 years breeding cows,” cautioned Will. “Don’t ignore the phenotype of an animal and simply chase a number.”

This article appears in the September 10, 2011 issue of Hoard's Dairyman on page 564.